Jonathan Cooper

According to our database, Jonathan Cooper authored at least 24 papers between 1993 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

CellML 2.0.1.

Michael Clerx, Michael T. Cooling, Jonathan Cooper, Alan Garny, Keri R. Moyle, David P. Nickerson, Poul M. F. Nielsen, Hugh Sorby

J. Integr. Bioinform., March, 2023

"A Switch Went off in my Whole Body": Lived Experiences of Fatigue and Post-Exertional Malaise in Long Covid.

Corina Sas, Yojana Lotankar, Rosalind Adam, Katherine J. Bradbury, Jonathan Cooper, Derek L. Hill, Veronica Martinez, Daniel Powell

Proceedings of the Extended Abstracts of the 2023 CHI Conference on Human Factors in Computing Systems, 2023

2020

Chaste: Cancer, Heart and Soft Tissue Environment.

Fergus R. Cooper, Ruth E. Baker, Miguel O. Bernabeu, Rafel Bordas, Louise Bowler, Alfonso Bueno-Orovio, Helen M. Byrne, Valentina Carapella, Louie Cardone-Noott, Jonathan Cooper, Sara Dutta, Benjamin D. Evans, Alexander G. Fletcher, James A. Grogan, Wenxian Guo, Daniel G. Harvey, Maurice Hendrix, David Kay, Jochen Kursawe, Philip K. Maini, Beth McMillan, Gary R. Mirams, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, Martin Robinson, Blanca Rodríguez, Raymond J. Spiteri, David Gavaghan

J. Open Source Softw., 2020

CellML 2.0.

Michael Clerx, Michael T. Cooling, Jonathan Cooper, Alan Garny, Keri R. Moyle, David P. Nickerson, Poul M. F. Nielsen, Hugh Sorby

J. Integr. Bioinform., 2020

2019

Fault-tolerant control for commercial aircraft with actuator faults and constraints.

Yishi Liu, Xiwang Dong, Zhang Ren, Jonathan Cooper

J. Frankl. Inst., 2019

2018

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

Frank T. Bergmann, Jonathan Cooper, Matthias König, Ion I. Moraru, David P. Nickerson, Nicolas Le Novère, Brett G. Olivier, Sven Sahle, Lucian P. Smith, Dagmar Waltemath

J. Integr. Bioinform., 2018

2016

Where next for the reproducibility agenda in computational biology?

Joanna Lewis, Charles E. Breeze, Jane Charlesworth, Oliver J. Maclaren, Jonathan Cooper

BMC Syst. Biol., 2016

2015

Ten Simple Rules for a Successful Cross-Disciplinary Collaboration.

Bernhard Knapp, Rémi Bardenet, Miguel O. Bernabeu, Rafel Bordas, Maria Bruna, Ben Calderhead, Jonathan Cooper, Alexander G. Fletcher, Derek Groen, Bram Kuijper, Joanna Lewis, Greg J. McInerny, Timo Minssen, James M. Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A. Yates, David Gavaghan, Charlotte M. Deane

PLoS Comput. Biol., 2015

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Frank T. Bergmann, Jonathan Cooper, Nicolas Le Novère, David P. Nickerson, Dagmar Waltemath

J. Integr. Bioinform., 2015

2014

Ten Simple Rules for Effective Computational Research.

James M. Osborne, Miguel O. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G. Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J. McInerny, Gary R. Mirams, Joe Pitt-Francis, Biswa Sengupta, David W. Wright, Christian A. Yates, David Gavaghan, Stephen Emmott, Charlotte M. Deane

PLoS Comput. Biol., 2014

Chaste: A case study of parallelisation of an open source finite-element solver with applications to computational cardiac electrophysiology simulation.

Miguel O. Bernabeu, James Southern, Nicholas Wilson, Peter E. Strazdins, Jonathan Cooper, Joe Pitt-Francis

Int. J. High Perform. Comput. Appl., 2014

COMBINE archive: One File To Share Them All.

Frank T. Bergmann, Richard Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère

CoRR, 2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

Frank T. Bergmann, Richard R. Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère

BMC Bioinform., 2014

2013

Chaste: An Open Source C++ Library for Computational Physiology and Biology.

Gary R. Mirams, Christopher J. Arthurs, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G. Fletcher, Daniel G. Harvey, Megan E. Marsh, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, David Gavaghan

PLoS Comput. Biol., 2013

Connecting Models to Data in Multiscale Multicellular Tissue Simulations.

Jonathan Cooper, James M. Osborne

Proceedings of the International Conference on Computational Science, 2013

2011

Minimum Information About a Simulation Experiment (MIASE).

Dagmar Waltemath, Richard R. Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Mike T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère

PLoS Comput. Biol., 2011

TumorML: Concept and requirements of an in silico cancer modelling markup language.

David Johnson, Jonathan Cooper, Steve McKeever

Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011

2010

A Posteriori Error Analysis for the Use of Lookup Tables in Cardiac Electrophysiology Simulations.

Jonathan Cooper, Jonathan P. Whiteley, David J. Gavaghan

SIAM J. Sci. Comput., 2010

An overview of the CellML API and its implementation.

Andrew K. Miller, Justin Marsh, Adam Reeve, Alan Garny, Randall Britten, Matt D. B. Halstead, Jonathan Cooper, David P. Nickerson, Poul M. F. Nielsen

BMC Bioinform., 2010

2009

Chaste: A test-driven approach to software development for biological modelling.

Joe Pitt-Francis, Pras Pathmanathan, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alexander G. Fletcher, Gary R. Mirams, Philip J. Murray, James M. Osborne, Alex Walter, S. Jonathan Chapman, Alan Garny, Ingeborg M. M. van Leeuwen, Philip K. Maini, Blanca Rodríguez, Sarah L. Waters, Jonathan P. Whiteley, Helen M. Byrne, David Gavaghan

Comput. Phys. Commun., 2009

2008

A model-driven approach to automatic conversion of physical units.

Jonathan Cooper, Steve McKeever

Softw. Pract. Exp., 2008

2007

Experience report: a Haskell interpreter for cellML.

Jonathan Cooper, Steve McKeever

Proceedings of the 12th ACM SIGPLAN International Conference on Functional Programming, 2007

2006

On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations.

Jonathan Cooper, Steve McKeever, Alan Garny

Proceedings of the 2006 ACM SIGPLAN Workshop on Partial Evaluation and Semantics-based Program Manipulation, 2006

1993

Engaging the Visitor: Relevance, Participation and Motivation in Hypermedia Design.

Jonathan Cooper

Proceedings of the Museums and Interactive Multimedia. Proceedings of the Sixth International Conference of the MDA and the Second International Conference on Hypermedia and Interactivity in Museums, 1993